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(-) Description

Title :  4M5.3 ANTI-FLUORESCEIN SINGLE CHAIN ANTIBODY FRAGMENT (SCFV)
 
Authors :  K. S. Midelfort, H. H. Hernandez, S. M. Lippow, B. Tidor, C. L. Drennan, K. D. Wittrop
Date :  24 Aug 04  (Deposition) - 22 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Very High Affinity, Antibody Binding, Electrostatics, Directed Evolution, Single Chain Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. S. Midelfort, H. H. Hernandez, S. M. Lippow, B. Tidor, C. L. Drennan, K. D. Wittrop
Substantial Energetic Improvement With Minimal Structural Perturbation In A High Affinity Mutant Antibody
J. Mol. Biol. V. 343 685 2004
PubMed-ID: 15465055  |  Reference-DOI: 10.1016/J.JMB.2004.08.019
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 4M5.3 ANTI-FLUORESCEIN SINGLE CHAIN ANTIBODY FRAGMENT
    Chains: A
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Common: BAKER'S YEAST
    Expression System Plasmid: GAL1-10 PROMOTER
    Expression System Strain: YVH10
    Expression System Taxid: 4932
    Expression System Vector Type: PRS316
    Fragment: ANTIBODY BINDING FRAGMENT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SCFV

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2FLU1Ligand/Ion2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:182 , TYR A:254 , FLU A:1341BINDING SITE FOR RESIDUE ACT A 1474
2AC2SOFTWAREARG A:73 , VAL A:74 , SER A:75 , MET A:256 , HOH A:1548 , HOH A:1600BINDING SITE FOR RESIDUE ACT A 1475
3AC3SOFTWARELYS A:58 , ASP A:101BINDING SITE FOR RESIDUE ACT A 1476
4AC4SOFTWAREACT A:1478BINDING SITE FOR RESIDUE ACT A 1477
5AC5SOFTWAREVAL A:27 , GLU A:124 , ACT A:1477BINDING SITE FOR RESIDUE ACT A 1478
6AC6SOFTWAREHIS A:45 , TYR A:51 , ARG A:53 , SER A:110 , TRP A:115 , HIS A:182 , TRP A:184 , TYR A:207 , ALA A:252 , TYR A:254 , GLY A:255 , ACT A:1474 , HOH A:1563 , HOH A:1595 , HOH A:1598BINDING SITE FOR RESIDUE FLU A 1341

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:37 -A:107
2A:173 -A:249

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:21 -Pro A:22
2Val A:113 -Pro A:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X9Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X9Q)

(-) Exons   (0, 0)

(no "Exon" information available for 1X9Q)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains d1x9qa1 A:14-124 automated matches                                                                             ----d1x9qa2 A:153-268 automated matches                                                                                  SCOP domains
               CATH domains 1x9qA01 A:14-124 Immunoglobulins                                                                               1x9qA02 A:149-268 Immunoglobulins                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eee......eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeee.....eeeee..eee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee.hhhhh..eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeee..eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x9q A  14 SDVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLRWYLQKPGQSPKVLIYKVSNRVSGVPDRFSGSGSGTDFTLKINRVEAEDLGVYFCSQSTHVPWTFGGGTKLEKDGGVKLDETGGGLVQPGGAMKLSCVTSGFTFGHYWMNWVRQSPEKGLEWVAQFRNKPYNYETYYSDSVKGRFTISRDDSKSSVYLQMNNLRVEDTGIYYCTGASYGMEYLGQGTSVTVS 268
                                    23        33        43        53        63        73        83        93       103       113       123||     157       167       177       187       197       207       217       227       237       247       257       267 
                                                                                                                                        124|                                                                                                                       
                                                                                                                                         149
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1X9Q)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1X9Q)

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 Related Entries

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